World-class research into future sources of green energy is under threat in Britain from an environmental tax designed to boost energy efficiency and drive down carbon emissions, scientists claim.

Some facilities must find hundreds of thousands of pounds to settle green tax bills, putting jobs and research at risk.

The unexpected impact of the government's carbon reduction commitment (CRC) scheme is so severe that scientists and research funders have lobbied ministers for an exemption to reduce the bills.

Among the worst hit is the Culham Centre for Fusion Energy in Oxfordshire, a facility for research into almost limitless carbon-free energy. The lab faces an estimated £400,000 payment next year, raising the spectre of job losses and operational cuts. "Considering our research is aimed at producing zero-carbon energy, it seems ironic and perverse to clobber us with an extra bill," a senior scientist at the lab said. "We have to use electricity to run the machine and there is no way of getting around that."

The laboratory operates the Joint European Torus (JET), the largest fusion reactor in Europe. It has led the way in research on fusion energy. The Culham lab faces a significant bill because, while energy savings can be made in other areas of the site, the machine incurs a large electricity bill when it is running.

The Prospect union is urging the government to exempt energy use where the focus of research contributes directly to public good and government policy.

"This [tax] will have a negative impact on important research into low carbon energy sources and that cannot be the right consequence of a policy the government is pursuing to promote a low carbon economy," said Sue Ferns, head of research at Prospect. "There is a potential for the scheme to impact on employment and it adds to pressures to run the equipment less. Even if it doesn't lead to substantial job losses, these are world-class scientists and every job, every piece of research makes a difference."

Britain's main funding body for research centres, the Science and Technology Facilities Council, is trying to persuade ministers to rethink how the scheme applies to scientific laboratories. The STFC's bill will "inevitably" mean less funding for research across its centres, the Guardian has been told.

All representations have been dismissed by the government, but the chief scientist, Sir John Beddington, passed on researchers' concerns to the Department of Energy and Climate Change (DECC) for an ongoing review.

Across the UK, laboratories will be required to pay around £1m in annual CRC bills to the DECC. Almost all of that will be met by diverting grants from other areas of government, such as the Department for Business, Innovation and Skills.

In the October spending review, the government shelved plans to recycle money raised by the scheme to participants, and said it would instead earn £1bn in revenue to support public finances.

Another Oxfordshire laboratory, the Diamond synchrotron light source, expects a £300,000 bill under the CRC. A spokesman said the lab hoped to offset the bill by investing in better climate control and motion-sensitive lighting.

At the Daresbury laboratory in Cheshire, the CRC bill will worsen financial woes that have forced managers to draft redundancy packages and consider cutting back on equipment. "Science is already struggling here and now we are being charged an additional premium to go about our everyday business while working to address the government's own stated grand challenges in science for the 21st century.," said Lee Jones, an accelerator physicist at the laboratory.

The DECC said: "All parts of the UK economy will need to play a part in using energy more efficiently. The measures encouraged by the CRC can make organisations more competitive via the cost savings on their energy bills.

"We are working on simplifying the CRC scheme to make it more straightforward and reduce burden on participants. Further details of how we plan to do this will be published in the coming months."

UN's call to CO2 action

The fastest-ever rise in greenhouse gas emissions, revealed by the Guardian yesterday, is an "inconvenient truth" the world must face, the UN's climate change chief said.

Christiana Figueres, executive secretary of the UN framework convention, said: "This is the inconvenient truth of where human-generated greenhouse gas emissions are projected to go without much stronger international action, " she said, issuing a call ahead of UN talks in Bonn next week. "I won't hear that this is impossible."

Estimates from the International Energy Agency show that last year saw a record CO2 rise, despite the recession and government policies aimed at curbing greenhouse gases. Most came from emerging economies, including China, but there is evidence the west "exported" billions of tonnes of emissions. Fiona Harvey